193 lines
9.7 KiB
Groff
193 lines
9.7 KiB
Groff
LAMMPS (23 Oct 2017)
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using 1 OpenMP thread(s) per MPI task
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# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
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# Rigid CO2 TraPPE model
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# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
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# mixtures containing alkanes, carbon dioxide and
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# nitrogen AIChE J., 47,1676-1682 (2001)].
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# variables available on command line
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variable mu index -8.1
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variable disp index 0.5
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variable temp index 338.0
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variable lbox index 10.0
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variable spacing index 5.0
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# global model settings
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units real
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atom_style full
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boundary p p p
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pair_style lj/cut/coul/long 14
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pair_modify mix arithmetic tail yes
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kspace_style ewald 0.0001
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bond_style harmonic
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angle_style harmonic
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# box, start molecules on simple cubic lattice
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lattice sc ${spacing}
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lattice sc 5.0
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Lattice spacing in x,y,z = 5 5 5
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region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
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region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
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region box block 0 10.0 0 10.0 0 ${lbox} units box
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region box block 0 10.0 0 10.0 0 10.0 units box
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create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
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Created orthogonal box = (0 0 0) to (10 10 10)
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1 by 2 by 2 MPI processor grid
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molecule co2mol CO2.txt
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Read molecule co2mol:
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3 atoms with 2 types
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2 bonds with 1 types
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1 angles with 1 types
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0 dihedrals with 0 types
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0 impropers with 0 types
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create_atoms 0 box mol co2mol 464563 units box
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Created 24 atoms
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Time spent = 0.00261331 secs
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# rigid CO2 TraPPE model
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pair_coeff 1 1 0.053649 2.8
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pair_coeff 2 2 0.156973 3.05
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bond_coeff 1 0 1.16
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angle_coeff 1 0 180
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# masses
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mass 1 12.0107
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mass 2 15.9994
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# MD settings
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group co2 type 1 2
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24 atoms in group co2
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neighbor 2.0 bin
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neigh_modify every 1 delay 10 check yes
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velocity all create ${temp} 54654
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velocity all create 338.0 54654
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timestep 1.0
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# rigid constraints with thermostat
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fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
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fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
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fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
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8 rigid bodies with 24 atoms
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1.16 = max distance from body owner to body atom
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fix_modify myrigidnvt dynamic/dof no
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# gcmc
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variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
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fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
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fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
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# atom counts
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variable carbon atom "type==1"
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variable oxygen atom "type==2"
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group carbon dynamic all var carbon
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dynamic group carbon defined
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group oxygen dynamic all var oxygen
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dynamic group oxygen defined
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variable nC equal count(carbon)
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variable nO equal count(oxygen)
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# output
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variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
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variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
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variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
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variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
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compute_modify thermo_temp dynamic/dof yes
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thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
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thermo 1000
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# run
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run 20000
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Ewald initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.164636
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estimated absolute RMS force accuracy = 0.0332064
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estimated relative force accuracy = 0.0001
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KSpace vectors: actual max1d max3d = 16 2 62
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kxmax kymax kzmax = 2 2 2
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WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
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0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
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0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
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WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 16
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ghost atom cutoff = 16
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binsize = 8, bins = 2 2 2
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 15.41 | 15.41 | 15.41 Mbytes
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Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
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0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0 8 16
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WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
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1000 335.66829 -3.7743052 -4.6268612 7.3374649 0.36539744 15 0.20601899 0.20787963 0 0 5 10
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2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0 3 6
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3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0 13 26
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4000 182.70803 -1059.2262 -43.044833 12.163134 1.0231128 42 0.16781689 0.16716177 0 0 14 28
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5000 234.00907 -1821.0444 -46.04795 15.578317 1.0231128 42 0.13498091 0.13704201 0 0 14 28
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6000 163.42759 -774.67294 -49.686261 11.691518 1.0961923 45 0.11401677 0.11296973 0 0 15 30
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7000 171.64616 -355.23516 -49.323434 12.27947 1.0961923 45 0.098302308 0.098552065 0 0 15 30
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8000 251.29791 -905.47863 -37.841209 15.480807 0.95003334 39 0.086856972 0.08638658 0 0 13 26
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9000 143.69498 -849.95393 -49.073188 10.279858 1.0961923 45 0.078261061 0.077955243 0 0 15 30
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10000 239.35727 -1158.1879 -43.562047 15.934355 1.0231128 42 0.070789792 0.070807529 0 0 14 28
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11000 169.51213 -1574.7885 -51.125228 12.126803 1.0961923 45 0.065008734 0.06498871 0 0 15 30
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12000 181.39739 160.11631 -46.850937 12.977068 1.0961923 45 0.059648717 0.059514803 0 0 15 30
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13000 164.14601 -1107.7629 -50.726722 11.742914 1.0961923 45 0.055207333 0.055097701 0 0 15 30
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14000 287.26285 418.51463 -41.664766 19.123497 1.0231128 42 0.051346789 0.051222285 0 0 14 28
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15000 256.94593 -532.36615 -41.651618 17.105257 1.0231128 42 0.047870301 0.047861685 0 0 14 28
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16000 166.92132 151.15933 -39.957018 11.11219 1.0231128 42 0.045205599 0.045042211 0 0 14 28
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17000 163.22452 -1299.8119 -42.677558 10.866089 1.0231128 42 0.043122086 0.042993687 0 0 14 28
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18000 158.01154 475.77329 -48.803162 11.304057 1.0961923 45 0.041016683 0.040647229 0 0 15 30
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19000 138.49297 -1585.1508 -47.517099 9.9077098 1.0961923 45 0.038929287 0.038436764 0 0 15 30
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20000 173.84439 -1362.6301 -53.002743 12.436731 1.0961923 45 0.036973919 0.036523816 0 0 15 30
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Loop time of 32.4481 on 4 procs for 20000 steps with 45 atoms
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Performance: 53.254 ns/day, 0.451 hours/ns, 616.369 timesteps/s
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98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 1.1687 | 1.6702 | 2.1864 | 30.8 | 5.15
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Bond | 0.018828 | 0.020035 | 0.020975 | 0.6 | 0.06
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Kspace | 0.57506 | 1.0931 | 1.5898 | 37.7 | 3.37
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Neigh | 0.068863 | 0.069524 | 0.070128 | 0.2 | 0.21
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Comm | 2.0735 | 2.0865 | 2.0979 | 0.7 | 6.43
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Output | 0.0025017 | 0.0025966 | 0.0027781 | 0.2 | 0.01
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Modify | 27.335 | 27.344 | 27.363 | 0.2 | 84.27
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Other | | 0.1621 | | | 0.50
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Nlocal: 11.25 ave 14 max 8 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Nghost: 2639.75 ave 2656 max 2617 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 4320 ave 5824 max 2201 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Total # of neighbors = 17280
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Ave neighs/atom = 384
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Ave special neighs/atom = 2
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Neighbor list builds = 20394
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Dangerous builds = 0
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Total wall time: 0:00:32
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